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(-) Description

Title :  STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (4R,6R,7S)-2-(2-CYCLOPROPYL)ETHYL-4,6,7-TRIHYDROXY-4,5,6,7-TETRAHYDROBENZO( B)THIOPHENE-4-CARBOXYLIC ACID
 
Authors :  S. Paz, L. Tizon, J. M. Otero, A. L. Llamas-Saiz, G. C. Fox, M. J. Van Raai A. R. Hawkins, L. Castedo, C. Gonzalez-Bello
Date :  30 Apr 10  (Deposition) - 24 Nov 10  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Keywords :  Aromatic Amino Acid Biosynthesis, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Paz, L. Tizon, J. M. Otero, A. L. Llamas-Saiz, G. C. Fox, M. J. Van Raaij, H. Lamb, A. R. Hawkins, L. Castedo, C. Gonzalez-Bello
Tetrahydrobenzothiophene Derivatives: Conformationally Restricted Inhibitors Of Type Ii Dehydroquinase.
Chemmedchem V. 6 266 2011
PubMed-ID: 21275050  |  Reference-DOI: 10.1002/CMDC.201000343

(-) Compounds

Molecule 1 - 3-DEHYDROQUINATE DEHYDRATASE
    Chains: A
    EC Number: 4.2.1.10
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210
    Synonym: 3-DEHYDROQUINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (12x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1JPS1Ligand/Ion(4R,6R,7S)-2-(2-CYCLOPROPYLETHYL)-4,6,7-TRIHYDROXY-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-4-CARBOXYLIC ACID
Biological Unit 1 (1, 12)
No.NameCountTypeFull Name
1JPS12Ligand/Ion(4R,6R,7S)-2-(2-CYCLOPROPYLETHYL)-4,6,7-TRIHYDROXY-4,5,6,7-TETRAHYDRO-1-BENZOTHIOPHENE-4-CARBOXYLIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:10 , MET A:13 , ARG A:17 , TYR A:22 , ASN A:76 , GLY A:78 , ALA A:79 , HIS A:82 , ASP A:89 , LEU A:93 , HIS A:102 , LEU A:103 , THR A:104 , ARG A:113BINDING SITE FOR RESIDUE JPS A1151

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XDA)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2XDA)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XDA)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IIPS01029 Dehydroquinase class II signature.AROQ_HELPY6-23  1A:6-23
Biological Unit 1 (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DEHYDROQUINASE_IIPS01029 Dehydroquinase class II signature.AROQ_HELPY6-23  12A:6-23

(-) Exons   (0, 0)

(no "Exon" information available for 2XDA)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:150
 aligned with AROQ_HELPY | Q48255 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
           AROQ_HELPY     1 MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFFQTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIEVHLTNIQAREEFRKNSYTGAACGGVIMGFGPLGYNMALMAMVNILAEMKA 150
               SCOP domains d2xdaa_ A: automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains DHquinase_II-2xdaA01 A:1-143                                                                                                                   ------- Pfam domains
         Sec.struct. author .eeeeee..hhhhh...hhhhhh..hhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhh..eeeee.......hhhhh.hhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----DEHYDROQUINASE_II ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2xda A   1 MKILVIQGPNLNMLGHRDPRLYGMVTLDQIHEIMQTFVKQGNLDVELEFFQTNFEGEIIDKIQESVGSDYEGIIINPGAFSHTSIAIADAIMLAGKPVIEVHLTNIQAREEFRKNSYTGAACGGVIMGFGPLGYNMALMAMVNILAEMKA 150
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2XDA)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: DHquinase_II] (16)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (AROQ_HELPY | Q48255)
molecular function
    GO:0003855    3-dehydroquinate dehydratase activity    Catalysis of the reaction: 3-dehydroquinate = 3-dehydroshikimate + H(2)O.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0009073    aromatic amino acid family biosynthetic process    The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
    GO:0008652    cellular amino acid biosynthetic process    The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
    GO:0009423    chorismate biosynthetic process    The chemical reactions and pathways resulting in the formation of the unsymmetrical ether derived from phosphoenolpyruvate and 5-phosphoshikimic acid formed as an intermediate in the biosynthesis of aromatic amino acids and many other compounds.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        AROQ_HELPY | Q48255: 1j2y 2c4v 2c4w 2c57 2wks 2xb9 2xd9 4b6r 4b6s

(-) Related Entries Specified in the PDB File

1j2y CRYSTAL STRUCTURE OF THE TYPE II 3- DEHYDROQUINASE
2c4v H. PYLORI TYPE II DHQASE IN COMPLEX WITH CITRATE
2c4w TYPE II DEHYDROQUINASE FROM H. PYLORI IN COMPLEX WITH AH9095
2c57 H.PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH FA1
2wks STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE WITH A NEW CARBASUGAR-THIOPHENE INHIBITOR.
2xb9 STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (2R)-2-(4-METHOXYBENZYL)-3- DEHYDROQUINIC ACID
2xd9 STRUCTURE OF HELICOBACTER PYLORI TYPE II DEHYDROQUINASE IN COMPLEX WITH INHIBITOR COMPOUND (4R,6R,7S)-4,6,7-TRIHYDROXY-2 -((E)-PROP-1-ENYL)-4,5,6,7- TETRAHYDROBENZO(B)THIOPHENE-4-CARBOXYLIC ACID